They are all out on 453.
Kagiso Rabada intervened with a three-wicket burst before lunch, removing Rahane for 58, Pujara for 53 and the dangerous Rishabh Pant for a duck.
Till date, India has never won a test series at South African soil, whereas South Africa has won a series in India when they toured in 1999.
India ended the day on a high after getting the crucial wicket of Dean Elgar at the stroke of Stumps.